James Gordon, Sr. is married to his wife, Barbara. They have a son (I don't remember the daughter from the comics, but they retcon things all the time).

One day, Barbara and James Jr get kidnapped by the Joker and put in a warehouse full of babies. I think Barbara saves all the babies ('cept her son) and then gets blown up. Or something. I need to find it for real. Right around that time Jim's niece loses her parents in a car accident, and Jim adopts her. Her name is Barbara. Confused yet? She becomes Batgirl. THAT IS WHAT HAPPENED TO INVISIBLE SON.